Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYCN

Cell type

Cell type Class
Neural
Cell type
SH-EP
NA
NA

Attributes by original data submitter

Sample

source_name
SHEP MYCN-ER
cell line
SHEP MYCN-ER
treatment
DMSO
antibody
N-MYC

Sequenced DNA Library

library_name
GSM6585370
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. For ChIP-seq, SHEP MYCN-ER cells were crosslinked with 1% paraformaldehyde for 10 minutes and were quenched with glycine for 5 minutes. After cell lysis, fixed chromatin was fragmented to 200-600 bp DNA size using a Diagenode Bruptor Plus. DNA fragments was immunoprecipitated with indicated antibodies and Protein A/G beads. Specific antibodies against MYCN, MAX, AFF1 and AFF4, were generated by immunization in rabbits with recombinant antigens. 1-10 ng of immunoprecipitated DNA was used for DNA library preparation.

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
18315889
Reads aligned (%)
41.5
Duplicates removed (%)
23.7
Number of peaks
4281 (qval < 1E-05)

hg19

Number of total reads
18315889
Reads aligned (%)
41.2
Duplicates removed (%)
23.9
Number of peaks
4259 (qval < 1E-05)

Base call quality data from DBCLS SRA